UPDATE: The Steam page for the Pixel Remaster has been published, the series will launch on Steam on July 28th with Final Fantasy and Final Fantasy II launching on the same day.
The versions of Final Fantasy V and VI being delisted from Steam were originally released in 2015 and based off of ports from mobile device versions that featured inconsistencies not found in the original console versions of the games.
The delisting does not affect the 3D versions of the games and they will remain available alongside the Pixel Remaster versions for the forseeable future.